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- PDB-3jwe: Crystal structure of human mono-glyceride lipase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3jwe
TitleCrystal structure of human mono-glyceride lipase in complex with SAR629
ComponentsMGLL protein
KeywordsHYDROLASE / alpha-beta hydrolase
Function / homology
Function and homology information


Arachidonate production from DAG / acylglycerol catabolic process / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / monoacylglycerol catabolic process / triglyceride catabolic process / regulation of endocannabinoid signaling pathway / acylglycerol lipase activity / arachidonic acid metabolic process / regulation of sensory perception of pain ...Arachidonate production from DAG / acylglycerol catabolic process / Acyl chain remodeling of DAG and TAG / acylglycerol lipase / monoacylglycerol catabolic process / triglyceride catabolic process / regulation of endocannabinoid signaling pathway / acylglycerol lipase activity / arachidonic acid metabolic process / regulation of sensory perception of pain / lysophospholipase activity / Triglyceride catabolism / regulation of signal transduction / lipid metabolic process / fatty acid biosynthetic process / regulation of inflammatory response / inflammatory response / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane / cytosol
Similarity search - Function
Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Lipases, serine active site. / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F4P / Monoglyceride lipase / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for human monoglyceride lipase inhibition.
Authors: Bertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MGLL protein
B: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7355
Polymers70,5852
Non-polymers1,1503
Water1,27971
1
A: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6762
Polymers35,2931
Non-polymers3831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0593
Polymers35,2931
Non-polymers7672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.821, 138.506, 127.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein MGLL protein / Monoglyceride lipase / isoform CRA_b / cDNA / FLJ96595 / Homo sapiens monoglyceride lipase (MGLL) / mRNA


Mass: 35292.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL, hCG_40840 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q6IBG9, UniProt: Q99685*PLUS, acylglycerol lipase
#2: Chemical ChemComp-F4P / 1-[bis(4-fluorophenyl)methyl]-4-(1H-1,2,4-triazol-1-ylcarbonyl)piperazine


Mass: 383.395 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H19F2N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsF4P 315 B IS AN UNCLEAVED FORM OF THE MOLECULE. F4P 314 A AND B IS THE RESULT OF THE CATALYTIC ...F4P 315 B IS AN UNCLEAVED FORM OF THE MOLECULE. F4P 314 A AND B IS THE RESULT OF THE CATALYTIC REACTION OCCURING IN THE CRYSTAL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES, 40% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2008
RadiationMonochromator: Diamonds 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→63.7 Å / Num. all: 18831 / Num. obs: 18831 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 52.05 Å2 / Rsym value: 0.104
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.356 / % possible all: 97

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JW8

3jw8


Resolution: 2.7→63.63 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 968 5.14 %RANDOM
Rwork0.1957 ---
all-18831 --
obs-18830 87.2 %-
Displacement parametersBiso mean: 39.08 Å2
Baniso -1Baniso -2Baniso -3
1--5.413 Å20 Å20 Å2
2---12.3252 Å20 Å2
3---17.7383 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.7→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 74 71 4408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.06
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.7→2.86 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2478 183 5.48 %
Rwork0.2141 3155 -
all0.2159 3338 -

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